# Write matrix table to a csv file **URL:** \ **Category:** Hail Query & hailctl\ **Created:** [October 20, 2021, 8:11pm UTC](https://discuss.hail.is/t/write-matrix-table-to-a-csv-file/2302 "2021-10-20T20:11:30Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![Jaden30](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/jaden30/32/501_2.png) [@Jaden30](https://discuss.hail.is/u/Jaden30)\ **Post date:** [October 20, 2021, 8:11pm UTC](https://discuss.hail.is/t/write-matrix-table-to-a-csv-file/2302/1 "2021-10-20T20:11:30Z")
Hi, Is it possible for me to write a matrix table to a csv file Thank you ---
**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\ **Post date:** [October 20, 2021, 9:14pm UTC](https://discuss.hail.is/t/write-matrix-table-to-a-csv-file/2302/2 "2021-10-20T21:14:26Z")
Hi @Jaden30 ! It sure is possible! The docs are hidden at [`Expression.export`](https://hail.is/docs/0.2/hail.expr.Expression.html#hail.expr.Expression.export): ```auto >>> small_mt.GT.export('output/gt.tsv') >>> with open('output/gt.tsv', 'r') as f: ... for line in f: ... print(line, end='') locus alleles 0 1 2 3 1:1 ["A","C"] 0/1 0/1 0/0 0/0 1:2 ["A","C"] 1/1 0/1 1/1 1/1 1:3 ["A","C"] 1/1 0/1 0/1 0/0 1:4 ["A","C"] 1/1 0/1 1/1 1/1 ``` You’ll want to use `delimiter=','` to get a CSV instead of a TSV. ---
**Author:** ![Jaden30](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/jaden30/32/501_2.png) [@Jaden30](https://discuss.hail.is/u/Jaden30)\ **Post date:** [October 20, 2021, 9:33pm UTC](https://discuss.hail.is/t/write-matrix-table-to-a-csv-file/2302/3 "2021-10-20T21:33:43Z")
Hi Danking, the examples in the code only show writing a field to a tsv/csv file, there are no ways for me to write the entire matrix table to a csv file? ---
**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\ **Post date:** [October 20, 2021, 10:31pm UTC](https://discuss.hail.is/t/write-matrix-table-to-a-csv-file/2302/4 "2021-10-20T22:31:52Z")
If you want to write the entire entry as a JSON object, that works: ```auto In [1]: import hail as hl ...: ...: mt = hl.balding_nichols_model(1, 3, 3) ...: mt = mt.annotate_entries(AD=5) ...: mt.entry.export('/tmp/bar.tsv') In [2]: !cat /tmp/bar.tsv locus alleles 0 1 2 1:1 ["A","C"] {"GT":"0/1","AD":5} {"GT":"1/1","AD":5} {"GT":"0/1","AD":5} 1:2 ["A","C"] {"GT":"1/1","AD":5} {"GT":"0/1","AD":5} {"GT":"1/1","AD":5} 1:3 ["A","C"] {"GT":"0/1","AD":5} {"GT":"0/0","AD":5} {"GT":"0/0","AD":5} ``` You can include more row fields by adding them to the key: ```auto In [4]: import hail as hl ...: ...: mt = hl.balding_nichols_model(1, 3, 3) ...: mt = mt.annotate_entries(AD=5) ...: non_key_row_fields = set(mt.row) - set(mt.row_key) ...: mt.key_rows_by(*mt.row_key, *non_key_row_fields).entry.export('/tmp/bar.tsv') In [5]: !cat /tmp/bar.tsv locus alleles af ancestral_af 0 1 2 1:1 ["A","C"] [0.44805795611590166] 5.39051e-01 {"GT":"0/1","AD":5} {"GT":"0/1","AD":5} {"GT":"0/1","AD":5} 1:2 ["A","C"] [0.7042578478282053] 8.67678e-01 {"GT":"1/1","AD":5} {"GT":"1/1","AD":5} {"GT":"1/1","AD":5} 1:3 ["A","C"] [0.35246827252547935] 4.37646e-01 {"GT":"0/1","AD":5} {"GT":"0/0","AD":5} {"GT":"0/1","AD":5} ``` If you don’t want JSON for entries, you can do this, admittedly very ugly, thing: ```auto In [23]: import hail as hl ...: ...: mt = hl.balding_nichols_model(1, 3, 3) ...: mt = mt.annotate_entries(AD=5) ...: mt = mt.annotate_cols(entry_id=list(range(len(mt.entry)))) ...: mt = mt.explode_cols(mt.entry_id) ...: mt = mt.key_cols_by(sample_id = hl.str(mt.sample_idx) + hl.literal('_') + hl.literal(list(mt.entry))[mt.entry_id]) ...: mt = mt.select_entries(entries_as_str = [hl.str(mt[f]) for f in mt.entry]) ...: mt = mt.select_entries(the_entry=mt.entries_as_str[mt.entry_id]) ...: non_key_row_fields = set(mt.row) - set(mt.row_key) ...: mt.key_rows_by(*mt.row_key, *non_key_row_fields).the_entry.export('/tmp/bar.tsv') In [22]: !cat /tmp/bar.tsv locus alleles af ancestral_af 0_GT 0_AD 1_GT 1_AD 2_GT 2_AD 1:1 ["A","C"] [0.5383546190066579] 5.39051e-01 0/1 5 0/0 5 0/1 5 1:2 ["A","C"] [0.9595560241510789] 8.67678e-01 1/1 5 0/1 5 1/1 5 1:3 ["A","C"] [0.5301809406988318] 4.37646e-01 0/1 5 0/0 5 0/1 5 ``` As for the column fields, you cannot include those in the CSV. I’m not really sure how to do that in CSV? I would store the column fields in a separate CSV file. Also, be ware that commas often appear in the JSON that Hail generates for non-scalar fields like the alleles list. ---
**Author:** ![Jaden30](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/jaden30/32/501_2.png) [@Jaden30](https://discuss.hail.is/u/Jaden30)\ **Post date:** [October 21, 2021, 12:26pm UTC](https://discuss.hail.is/t/write-matrix-table-to-a-csv-file/2302/5 "2021-10-21T12:26:33Z")
Thank you very much for your response ```auto Traceback (most recent call last): File "transvcf.py", line 66, in fire.Fire(VCF) File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/fire/core.py", line 141, in Fire component_trace = _Fire(component, args, parsed_flag_args, context, name) File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/fire/core.py", line 471, in _Fire target=component. __name__ ) File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/fire/core.py", line 681, in _CallAndUpdateTrace component = fn(*varargs, **kwargs) File "transvcf.py", line 50, in identify_AF dataset = hl.import_vcf(vcf, skip_invalid_loci = True, array_elements_required=False) File "", line 2, in import_vcf File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/hail/typecheck/check.py", line 576, in wrapper args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method) File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/hail/typecheck/check.py", line 543, in check_all args_.append(arg_check(args[i], name, arg_name, checker)) File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/hail/typecheck/check.py", line 584, in arg_check return checker.check(arg, function_name, arg_name) File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/hail/typecheck/check.py", line 82, in check return tc.check(x, caller, param) File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/hail/typecheck/check.py", line 328, in check return f(tc.check(x, caller, param)) File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/hail/genetics/reference_genome.py", line 10, in reference_genome_type = oneof(transformed((str, lambda x: hl.get_reference(x))), rg_type) File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/hail/context.py", line 554, in get_reference Env.hc() File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/hail/utils/java.py", line 55, in hc init() File "", line 2, in init File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/hail/typecheck/check.py", line 577, in wrapper return __original_func(*args_, **kwargs_) File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/hail/context.py", line 252, in init skip_logging_configuration, optimizer_iterations) File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/hail/backend/spark_backend.py", line 176, in __init__ self._jbackend, log, True, append, branching_factor, skip_logging_configuration, optimizer_iterations) File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/py4j/java_gateway.py", line 1305, in __call__ answer, self.gateway_client, self.target_id, self.name) File "/Users/jaden/miniconda3/envs/hail/lib/python3.7/site-packages/py4j/protocol.py", line 328, in get_return_value format(target_id, ".", name), value) py4j.protocol.Py4JJavaError: An error occurred while calling z:is.hail.HailContext.apply. : is.hail.utils.HailException: Hail requires Java ``` I had that error when running hail, I do not understand it or know how to fix it, can anybody help. Thank you ---
**Author:** ![johnc1231](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/johnc1231/32/286_2.png) [@johnc1231](https://discuss.hail.is/u/johnc1231)\ **Post date:** [October 21, 2021, 12:29pm UTC](https://discuss.hail.is/t/write-matrix-table-to-a-csv-file/2302/6 "2021-10-21T12:29:38Z")
Did you install Java? It’s listed in our installation instructions: [Hail | Installing Hail](https://hail.is/docs/0.2/getting_started.html) ---
**Author:** ![Jaden30](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/jaden30/32/501_2.png) [@Jaden30](https://discuss.hail.is/u/Jaden30)\ **Post date:** [October 21, 2021, 1:52pm UTC](https://discuss.hail.is/t/write-matrix-table-to-a-csv-file/2302/7 "2021-10-21T13:52:21Z")
Yes i have using the instructions. Still returning the error ---
**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\ **Post date:** [October 21, 2021, 3:16pm UTC](https://discuss.hail.is/t/write-matrix-table-to-a-csv-file/2302/8 "2021-10-21T15:16:34Z")
> [@Jaden30](#): > > `Hail requires Java` This looks like it’s missing part of the message. It should say something like: > Hail requires Java 8 or 11, found 12 What version of java (`java -version`) do you have installed?