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I imported a CSV file that uses commas as its delimiter, but some fields also contain commas. When I import the file into Mathematica as follows 

file = Import["file.csv", "Table", FieldSeparators -> ","]

It works and outputs stuff like this

{{"Epitope ID", "Sequence", "Mapped Start Position", "Mapped End Position", "Identity", "Subjects Tested", "Subjects Responded", "Assays Positive", "Assays Negative", "Response Freq.", "Lower Bound of 95% CI", "Upper Bound of 95% CI"}, {150975, "DTLCIGYHANNSTDT", 18, 32, "93.33%", 11, 5, 1, 0, 0.45, 0.2, 0.72}, {35073, "LCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKI", 20, 58, "30.77%", 1, 1, 1, 0, 1., 0.04, 1.}, {6570, "CLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKIC", 21, 59, "33.33%", 1, 1, 1, 0, 1., 0.04, 1.}, {191055, "H25, H45, I361, D362", 25, 362, "100%", 1, 1, 1, 0, 1., 0.04, 1.}, {434783, "H25, H45, S46, V47, T332, V361, D362, G363, W364, Q381, K382, \ T384, Q385, I388, N389, V395, N396, I399", 25, 399, "94.44%", 1, 1, 1, 0, 1., 0.04, 1.}, {434784, "H25, H45, V47, N48, L49, T332, D362, G363, W364, Q381, T384, Q385, \ I388, N389, T392, V395, N396, I399, E400", 25, 400, "100%", 1, 1, 1, 0, 1., 0.04, 1.}, {151039, "NSTDTVDTVLEKNVT", 28, 42, "100%", 11, 4, 1, 0, 0.36, 0.13, 0.64}, {417980, "D31, S46", 31, 46, "100%", 1, 1, 1, 0, 1., 0.04, 1.}, {580001, "D31, H45, S46, V47, T305, S306, T333, V362, D363, W365, L382, \ Q386, V396, N397", 31, 396, "78.57%", 1, 1, 1, 0, 1., 0.04, 1.},...}

If I put it in a TableView[file] it displays the data correctly. If I extract column 1, elements are formatted correctly in the resulting list. But if I extract column 2, which contains commas, it breaks each row into multiple elements.

How can I get Mathematica to identify each row as it is shown in the table? Those rows with commas would be sublists.

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  • $\begingroup$ Why use the "Table" format and not the "CSV" format? $\endgroup$ Commented Jan 30, 2019 at 16:00

1 Answer 1

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By default, quotation marks are shown around strings in input cells, but not in output cells. *

Since the quotation marks are not displayed, elements look as if they are broken:

file[[All, 2]]

enter image description here

To see that they are not broken, you can use

InputForm @ file[[All, 2]]

enter image description here

Update: If you need to transform strings containing commas into lists, you can use StringSplit:

StringSplit[file[[All, 2]], ","] /. {s_String} :> s

{"Sequence", "DTLCIGYHANNSTDT", "LCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKI", "CLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKIC", {"H25", " H45", " I361", " D362"}, {"H25", " H45", " S46", " V47", " T332", " V361", " D362", " G363", " W364", " Q381", " K382", " T384", " Q385", " I388", " N389", " V395", " N396", " I399"}, {"H25", " H45", " V47", " N48", " L49", " T332", " D362", " G363", " W364", " Q381", " T384", " Q385", " I388", " N389", " T392", " V395", " N396", " I399", " E400"}, "NSTDTVDTVLEKNVT", {"D31", " S46"}, {"D31", " H45", " S46", " V47", " T305", " S306", " T333", " V362", " D363", " W365", " L382", " Q386", " V396", " N397"}}

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  • $\begingroup$ I'm still looking at the docs for how to work with this -- I can't seem to access an InputForm object like a list, so how could I work with this? $\endgroup$ Commented Oct 5, 2018 at 22:49
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    $\begingroup$ @briennakh, please see the update. $\endgroup$ Commented Oct 5, 2018 at 22:58
  • $\begingroup$ Thank you, you're amazing!! @kglr $\endgroup$ Commented Oct 5, 2018 at 23:02

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