generate a header row using python's csv.writer

Question

I have a bit of python code that produces a .csv file, however I don't know how to add column names, or a header row. Here is my code:

handle = open(sys.argv[1])
with open('protparams.csv', 'w') as fp: 
    writer = csv.writer(fp, delimiter=',')
    for record in SeqIO.parse(handle, "fasta"): 
            seq = str(record.seq)
            X = ProtParam.ProteinAnalysis(seq)
            data = [seq,X.get_amino_acids_percent(),X.aromaticity(),X.gravy(),X.isoelectric_point(),X.secondary_structure_fraction(),X.molecular_weight(),X.instability_index()]
            writer.writerow(data)

I have tried adding in something like:

writer = csv.writer(fp, delimiter=',',[seq,aa_percentage,aromaticity,gravy,isoelectric_point,secondary_structure_fraction,molecular_weight,instability_index])

but this obviously doesn't work

anyone have any ideas?

Deelaka · Accepted Answer · 2014-06-15 15:32:23Z

2

Write the headers before the loop:

handle = open(sys.argv[1])
with open('protparams.csv', 'w') as fp:
    writer = csv.writer(fp, delimiter=',')
    writer.writerow(['heading1','heading2','heading3'])
    for record in SeqIO.parse(handle, "fasta"):
            seq = str(record.seq)
            X = ProtParam.ProteinAnalysis(seq)
            data = [seq,X.get_amino_acids_percent(),X.aromaticity(),X.gravy(),X.isoelectric_point(),X.secondary_structure_fraction(),X.molecular_weight(),X.instability_index()]
            writer.writerow(data)

edited Jun 15, 2014 at 15:32

answered Jun 15, 2014 at 15:11

Deelaka

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1 Comment

brucezepplin Over a year ago

ah so simple, how I didn't see it.

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