useful_short_scripts

A collection of short scripts that do useful stuff for bioinformatics and biodiversity informatics. Usage: copy and paste script in (Linux) terminal, rename input and output file names and hit enter.

Convert .fasta to .csv

Python script to be run directly in the shell. It adds column headers 'id' and 'sequence'. Replace ',' by '\t' to obtain a tab-delimited file.

fasta_to_csv () {
    PYCMD=$(cat <<EOF
fasta = 'input.fasta'
output = 'output.csv'

out_lines = []
temp_line = ''
with open(fasta, 'r') as fp:
    for line in fp:
        if line.startswith('>'):
            out_lines.append(temp_line)
            temp_line = line.strip() + ','
        else:
            temp_line += line.strip()
out_lines.append(temp_line)

with open(output, 'w') as fp_out:
    fp_out.write('id,sequence' + '\n'.join(out_lines))
EOF
    )

    python3 -c "$PYCMD"
}
fasta_to_csv

Convert .csv to .fasta

Python script to be run directly in the shell.

csv_to_fasta () {
    PYCMD=$(cat <<EOF
csv = 'input.csv'
output = 'output.fasta'

out_lines = []
temp_line = ''
with open(csv, 'r') as csv:
    for line in csv:
        cols = line.split(",")
        out_lines.append(temp_line)
        temp_line = ">" + cols[0] + "\n" + cols[1] + "\n"

out_lines.append(temp_line)

with open(output, 'w') as csv_out:
    csv_out.write(''.join(out_lines)[13:])
EOF
    )

    python3 -c "$PYCMD"
}
csv_to_fasta

Convert .fastq to .fasta

sed -n '1~4s/^@/>/p;2~4p' input.fastq > output.fasta

Reverse complement sequences in a .fasta file

Only works for sequences that do not contain gaps (-).

while read line; do
    if [[ $line =~ ">" ]]; then
        echo $line
    else
        echo $line | tr ACGTRYSWKMBDHVNacgtryswkmbdhvn TGCAYRWSMKVHDBNtgcayrwsmkvhdbn | rev
    fi
done < input.fasta > output.fasta

Merge two tables by common column

merge_tables () {
    PYCMD=$(cat <<EOF

import pandas as pd

df_table1 = pd.read_csv("table1.csv", sep=',')
df_table2 = pd.read_csv("table2.csv", sep=',')

combined = pd.merge(df_table1, df_table2, on=['common_column_name'])

combined.to_csv("output.csv", sep=',')

EOF
    )

    python3 -c "$PYCMD"
}
merge_tables